Do all your work from a single PP project in the same AE project. Don't create a new AE project for each comp.
I would much rather work with multiple AE comps in different AE projects from within the Premiere project. It is far more efficient.
The current project contains 43 clips in the sequence, all 1080p HD, of varient lengths. One AE project creates (or one comp) a project where I have to load 43 different layers (or pre-comps) within AE. Add effects, nested layers or solids and I have layer soup.
As Fuzzy shows in his screenshot, using multiple AE projects (comps) is a viable alternative from within Premiere. (Or should be.)
Moreover, the cure for the bug is pretty simple: re-render Entire Work Area when PrPro looses its way.
If this option is grey, select any clip on the timeline and just copy it into clipboard (Ctrl+C / Cmd+C) - Voilà ! Option is accessible.
No needs to rename or rebuild your AE comps.
No dependency on where to store AE projects.
It is far more efficient.
It also creates problems like the one you're having.
Work with all comps in one project, things fare better.